Contacts of the helix formed by residues 137 - 149 (chain C) in PDB entry 1M6X
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 137 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138C SER* 1.3 75.1 + - - +
139C HIS* 3.1 9.2 + - - +
140C SER* 3.3 21.7 + - - +
141C LYS* 3.1 41.0 + - - +
12G T 4.7 17.8 + - - +
13G C 3.7 14.6 + - - -
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Residues in contact with SER 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ASN* 3.0 25.6 + - - -
137C ASN* 1.3 84.8 + - - +
139C HIS* 1.3 68.5 + - - +
141C LYS* 3.4 9.5 + - - +
142C LYS* 3.2 21.7 + - - +
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Residues in contact with HIS 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ASN* 4.5 11.4 - - - +
137C ASN 4.2 4.7 - - - +
138C SER* 1.3 81.8 + - - +
140C SER* 1.3 61.8 + - - +
142C LYS* 3.1 10.4 + - + +
143C MET* 2.9 61.3 + - + +
298C ILE* 4.1 21.0 - - + +
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Residues in contact with SER 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ASN* 3.3 15.7 + - - -
139C HIS* 1.3 78.2 - - - +
141C LYS* 1.3 58.5 + - - +
143C MET* 3.2 1.9 + - - +
144C LEU* 2.8 30.7 + - - +
295C ILE* 3.8 6.0 - - - +
298C ILE* 3.6 33.3 - - - +
299C LYS 5.2 0.3 + - - -
300C ASN 5.2 0.2 - - - -
301C GLY* 3.9 11.4 - - - -
302C PRO* 4.3 19.7 - - - -
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Residues in contact with LYS 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ASN* 3.1 40.7 + - - +
138C SER* 3.7 10.3 - - - +
139C HIS 3.2 0.8 - - - -
140C SER* 1.3 79.3 - - - +
142C LYS* 1.3 61.9 + - - +
144C LEU* 3.5 9.0 + - + +
145C LYS* 3.1 20.4 + - - +
13G C 4.5 7.5 + - - -
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Residues in contact with LYS 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ASN* 5.0 13.4 + - - +
138C SER 3.2 10.1 + - - +
139C HIS* 3.1 14.4 + - + +
141C LYS* 1.3 76.5 - - - +
143C MET* 1.3 61.0 + - + +
145C LYS* 3.1 18.3 - - + +
146C ALA* 3.0 26.3 + - - +
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Residues in contact with MET 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C HIS* 2.9 50.0 + - + +
140C SER 3.5 4.5 - - - +
142C LYS* 1.3 75.8 - - + +
144C LEU* 1.3 60.3 + - - +
146C ALA* 3.2 12.4 + - - +
147C LEU* 2.8 29.0 + - - +
294C PRO* 4.2 30.3 - - + +
295C ILE* 3.8 20.0 - - + +
298C ILE* 3.5 15.9 - - + -
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Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C SER 2.8 16.7 + - - +
141C LYS* 3.8 8.7 - - - +
143C MET* 1.3 72.1 - - - +
145C LYS* 1.3 69.3 + - - +
147C LEU* 3.2 23.7 + - + +
148C LEU* 2.9 57.4 + - + +
295C ILE* 4.2 8.0 - - + +
302C PRO* 6.1 4.9 - - + -
306C ILE* 4.9 10.1 - - + -
309C HIS* 4.0 37.2 - - + -
310C LEU* 5.5 1.6 - - + -
313C SER* 5.0 3.4 - - - +
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Residues in contact with LYS 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A LYS* 2.8 32.2 - - - +
141C LYS 3.1 11.5 + - - +
142C LYS* 3.1 21.8 - - + +
144C LEU* 1.3 80.8 - - - +
146C ALA* 1.3 53.2 + - - +
148C LEU* 3.1 8.5 + - - +
149C SER* 2.6 56.3 + - - +
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Residues in contact with ALA 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C LYS 3.0 12.4 + - - +
143C MET* 3.3 17.7 - - - +
145C LYS* 1.3 78.5 - - - +
147C LEU* 1.3 67.0 + - - +
148C LEU 2.8 1.6 + - - -
149C SER* 3.0 6.6 + - - +
150C GLU* 2.9 40.1 - - - +
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Residues in contact with LEU 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C MET 2.8 15.7 + - - +
144C LEU* 3.2 31.2 - - + +
146C ALA* 1.3 73.0 - - - +
148C LEU* 1.3 66.5 + - + +
150C GLU* 4.2 14.9 + - - +
152C GLU* 4.8 1.6 - - - +
157C ILE* 3.6 36.6 - - + +
161C ILE* 6.3 0.7 - - + -
293C TYR* 3.9 32.8 - - + -
294C PRO* 6.1 5.4 - - + -
295C ILE* 4.5 16.8 - - + -
296C PHE* 6.0 0.9 - - + -
306C ILE* 4.3 18.6 - - + -
310C LEU* 4.8 6.5 - - + -
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Residues in contact with LEU 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C LEU* 2.9 43.8 + - + +
145C LYS* 3.4 8.1 - - - +
146C ALA 2.8 2.4 + - - -
147C LEU* 1.3 78.5 - - + +
149C SER* 1.3 55.1 + - - +
150C GLU 2.5 29.1 + - - +
152C GLU 4.2 4.3 - - - +
154C ILE* 3.8 29.2 - - + -
157C ILE* 4.8 4.0 - - + -
310C LEU* 4.3 8.7 - - + -
313C SER* 3.5 27.6 - - - +
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Residues in contact with SER 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C LYS* 2.6 44.9 + - - +
146C ALA* 4.1 2.5 - - - -
148C LEU* 1.3 68.8 - - - +
150C GLU* 1.3 66.5 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il